1.Integrated Transcriptomic Landscape and Deep Learning Based Survival Prediction in Uterine Sarcomas
Yaolin SONG ; Guangqi LI ; Zhenqi ZHANG ; Yinbo LIU ; Huiqing JIA ; Chao ZHANG ; Jigang WANG ; Yanjiao HU ; Fengyun HAO ; Xianglan LIU ; Yunxia XIE ; Ding MA ; Ganghua LI ; Zaixian TAI ; Xiaoming XING
Cancer Research and Treatment 2025;57(1):250-266
Purpose:
The genomic characteristics of uterine sarcomas have not been fully elucidated. This study aimed to explore the genomic landscape of the uterine sarcomas (USs).
Materials and Methods:
Comprehensive genomic analysis through RNA-sequencing was conducted. Gene fusion, differentially expressed genes (DEGs), signaling pathway enrichment, immune cell infiltration, and prognosis were analyzed. A deep learning model was constructed to predict the survival of US patients.
Results:
A total of 71 US samples were examined, including 47 endometrial stromal sarcomas (ESS), 18 uterine leiomyosarcomas (uLMS), three adenosarcomas, two carcinosarcomas, and one uterine tumor resembling an ovarian sex-cord tumor. ESS (including high-grade ESS [HGESS] and low-grade ESS [LGESS]) and uLMS showed distinct gene fusion signatures; a novel gene fusion site, MRPS18A–PDC-AS1 could be a potential diagnostic marker for the pathology differential diagnosis of uLMS and ESS; 797 and 477 uterine sarcoma DEGs (uDEGs) were identified in the ESS vs. uLMS and HGESS vs. LGESS groups, respectively. The uDEGs were enriched in multiple pathways. Fifteen genes including LAMB4 were confirmed with prognostic value in USs; immune infiltration analysis revealed the prognositic value of myeloid dendritic cells, plasmacytoid dendritic cells, natural killer cells, macrophage M1, monocytes and hematopoietic stem cells in USs; the deep learning model named Max-Mean Non-Local multi-instance learning (MMN-MIL) showed satisfactory performance in predicting the survival of US patients, with the area under the receiver operating curve curve reached 0.909 and accuracy achieved 0.804.
Conclusion
USs harbored distinct gene fusion characteristics and gene expression features between HGESS, LGESS, and uLMS. The MMN-MIL model could effectively predict the survival of US patients.
2.Integrated Transcriptomic Landscape and Deep Learning Based Survival Prediction in Uterine Sarcomas
Yaolin SONG ; Guangqi LI ; Zhenqi ZHANG ; Yinbo LIU ; Huiqing JIA ; Chao ZHANG ; Jigang WANG ; Yanjiao HU ; Fengyun HAO ; Xianglan LIU ; Yunxia XIE ; Ding MA ; Ganghua LI ; Zaixian TAI ; Xiaoming XING
Cancer Research and Treatment 2025;57(1):250-266
Purpose:
The genomic characteristics of uterine sarcomas have not been fully elucidated. This study aimed to explore the genomic landscape of the uterine sarcomas (USs).
Materials and Methods:
Comprehensive genomic analysis through RNA-sequencing was conducted. Gene fusion, differentially expressed genes (DEGs), signaling pathway enrichment, immune cell infiltration, and prognosis were analyzed. A deep learning model was constructed to predict the survival of US patients.
Results:
A total of 71 US samples were examined, including 47 endometrial stromal sarcomas (ESS), 18 uterine leiomyosarcomas (uLMS), three adenosarcomas, two carcinosarcomas, and one uterine tumor resembling an ovarian sex-cord tumor. ESS (including high-grade ESS [HGESS] and low-grade ESS [LGESS]) and uLMS showed distinct gene fusion signatures; a novel gene fusion site, MRPS18A–PDC-AS1 could be a potential diagnostic marker for the pathology differential diagnosis of uLMS and ESS; 797 and 477 uterine sarcoma DEGs (uDEGs) were identified in the ESS vs. uLMS and HGESS vs. LGESS groups, respectively. The uDEGs were enriched in multiple pathways. Fifteen genes including LAMB4 were confirmed with prognostic value in USs; immune infiltration analysis revealed the prognositic value of myeloid dendritic cells, plasmacytoid dendritic cells, natural killer cells, macrophage M1, monocytes and hematopoietic stem cells in USs; the deep learning model named Max-Mean Non-Local multi-instance learning (MMN-MIL) showed satisfactory performance in predicting the survival of US patients, with the area under the receiver operating curve curve reached 0.909 and accuracy achieved 0.804.
Conclusion
USs harbored distinct gene fusion characteristics and gene expression features between HGESS, LGESS, and uLMS. The MMN-MIL model could effectively predict the survival of US patients.
3.Integrated Transcriptomic Landscape and Deep Learning Based Survival Prediction in Uterine Sarcomas
Yaolin SONG ; Guangqi LI ; Zhenqi ZHANG ; Yinbo LIU ; Huiqing JIA ; Chao ZHANG ; Jigang WANG ; Yanjiao HU ; Fengyun HAO ; Xianglan LIU ; Yunxia XIE ; Ding MA ; Ganghua LI ; Zaixian TAI ; Xiaoming XING
Cancer Research and Treatment 2025;57(1):250-266
Purpose:
The genomic characteristics of uterine sarcomas have not been fully elucidated. This study aimed to explore the genomic landscape of the uterine sarcomas (USs).
Materials and Methods:
Comprehensive genomic analysis through RNA-sequencing was conducted. Gene fusion, differentially expressed genes (DEGs), signaling pathway enrichment, immune cell infiltration, and prognosis were analyzed. A deep learning model was constructed to predict the survival of US patients.
Results:
A total of 71 US samples were examined, including 47 endometrial stromal sarcomas (ESS), 18 uterine leiomyosarcomas (uLMS), three adenosarcomas, two carcinosarcomas, and one uterine tumor resembling an ovarian sex-cord tumor. ESS (including high-grade ESS [HGESS] and low-grade ESS [LGESS]) and uLMS showed distinct gene fusion signatures; a novel gene fusion site, MRPS18A–PDC-AS1 could be a potential diagnostic marker for the pathology differential diagnosis of uLMS and ESS; 797 and 477 uterine sarcoma DEGs (uDEGs) were identified in the ESS vs. uLMS and HGESS vs. LGESS groups, respectively. The uDEGs were enriched in multiple pathways. Fifteen genes including LAMB4 were confirmed with prognostic value in USs; immune infiltration analysis revealed the prognositic value of myeloid dendritic cells, plasmacytoid dendritic cells, natural killer cells, macrophage M1, monocytes and hematopoietic stem cells in USs; the deep learning model named Max-Mean Non-Local multi-instance learning (MMN-MIL) showed satisfactory performance in predicting the survival of US patients, with the area under the receiver operating curve curve reached 0.909 and accuracy achieved 0.804.
Conclusion
USs harbored distinct gene fusion characteristics and gene expression features between HGESS, LGESS, and uLMS. The MMN-MIL model could effectively predict the survival of US patients.
4.Analysis of the nonlinear relationship between hypothermic machine perfusion parameters and delayed graft function and construction of an optimized predictive model based on sampling algorithms
Boqing DONG ; Chongfeng WANG ; Yuting ZHAO ; Huanjing BI ; Ying WANG ; Jingwen WANG ; Zuhan CHEN ; Ruiyang MA ; Wujun XUE ; Yang LI ; Xiaoming DING
Organ Transplantation 2025;16(4):582-590
Objective To analyze the nonlinear relationship between hypothermic machine perfusion (HMP) parameters and delayed graft function (DGF) and optimize the construction of a predictive model for DGF. Methods The data of 923 recipients who underwent kidney transplantation from deceased donors were retrospectively analyzed. According to the occurrence of DGF, the recipients were divided into DGF group (n=823) and non-DGF group (n=100). Donor data, HMP parameters and recipient data were analyzed for both groups. The nonlinear relationship between HMP parameters and the occurrence of DGF was explored based on restricted cubic splines (RCS). Over-sampling, under-sampling and balanced sampling were used to address the imbalance in the proportion of DGF to construct logistic regression predictive models. The area under the curve (AUC) of each model was compared in the validation set, and a nomogram model was constructed. Results Donor BMI, cold ischemia time of the donor kidney, and HMP parameters (initial and final pressures, resistance, and perfusion time) were significantly different between the DGF and non-DGF groups (all P<0.05). The RCS analysis revealed a threshold-like nonlinear relationship between HMP parameters and the risk of DGF. Among the models constructed using different sampling methods, the balanced sampling model had the highest AUC. Using this model, a nomogram was constructed to stratify recipients based on risk scores. Recipients in the high-risk group had higher serum creatinine levels at 1, 6, and 12 months after kidney transplantation compared to those in the low-risk group (all P<0.05). Conclusions There is a nonlinear relationship between HMP parameters and the risk of DGF, and the threshold is helpful for organ quality assessment and monitoring of graft function after transplantation. The predictive model for DGF constructed on the base of balanced sampling algorithms helps perioperative decision-making and postoperative graft function monitoring of kidney transplantation.
5.Applications and prospects of graphene and its derivatives in bone repair.
Zhipo DU ; Yizhan MA ; Cunyang WANG ; Ruihong ZHANG ; Xiaoming LI
Chinese Journal of Reparative and Reconstructive Surgery 2025;39(1):106-117
OBJECTIVE:
To summarize the latest research progress of graphene and its derivatives (GDs) in bone repair.
METHODS:
The relevant research literature at home and abroad in recent years was extensively accessed. The properties of GDs in bone repair materials, including mechanical properties, electrical conductivity, and antibacterial properties, were systematically summarized, and the unique advantages of GDs in material preparation, functionalization, and application, as well as the contributions and challenges to bone tissue engineering, were discussed.
RESULTS:
The application of GDs in bone repair materials has broad prospects, and the functionalization and modification technology effectively improve the osteogenic activity and material properties of GDs. GDs can induce osteogenic differentiation of stem cells through specific signaling pathways and promote osteogenic activity through immunomodulatory mechanisms. In addition, the parameters of GDs have significant effects on the cytotoxicity and degradation behavior.
CONCLUSION
GDs has great potential in the field of bone repair because of its excellent physical and chemical properties and biological properties. However, the cytotoxicity, biodegradability, and functionalization strategies of GDs still need to be further studied in order to achieve a wider application in the field of bone tissue engineering.
Graphite/pharmacology*
;
Tissue Engineering/methods*
;
Humans
;
Osteogenesis/drug effects*
;
Biocompatible Materials/pharmacology*
;
Bone Regeneration
;
Tissue Scaffolds/chemistry*
;
Cell Differentiation
;
Bone and Bones
;
Bone Substitutes/chemistry*
;
Animals
6.PDZ-binding kinase as a prognostic biomarker for pancreatic cancer: a pan-cancer analysis and validation in pancreatic adenocarcinoma cells.
Jinguo WANG ; Yang MA ; Zhaoxin LI ; Lifei HE ; Yingze HUANG ; Xiaoming FAN
Journal of Southern Medical University 2025;45(10):2210-2222
OBJECTIVES:
To investigate the prognostic significance of PDZ-binding kinase (PBK) in pan-cancer and its potential as a therapeutic target for pancreatic cancer.
METHODS:
PBK expression levels were investigated in 33 cancer types based on data from TCGA, GEO and CPTAC databases. RT-PCR and Western blotting were employed to examine PBK expression in clinical pancreatic cancer specimens and cell lines. The diagnostic and prognostic value of PBK in pancreatic cancer was evaluated using survival analysis, Cox regression analysis, ROC curve analysis, and clinical correlation studies. Gene enrichment and immune correlation analyses were conducted to explore the potential role of PBK in tumor microenvironment, and its correlation with drug sensitivity was investigated using GDSC and CTRP datasets. In pancreatic cancer BXPC-3 cells, the effects of lentivirus-mediated PBK knockdown on cell proliferation, migration, and invasion were examined using CCK-8, colony formation, and Transwell assays. The interaction between PBK and non-SMC condensin II complex subunit G2 (NCAPG2) was analyzed using co-immunoprecipitation and Western blotting.
RESULTS:
PBK was overexpressed in multiple cancer types, including pancreatic cancer. A high PBK expression was associated with a poor prognosis of the patients and correlated with immune infiltration and alterations in the tumor microenvironment. Elevated PBK expression was positively correlated with the sensitivity to MEK inhibitors (Trametinib) and EGFR inhibitors (Afatinib) but negatively with the sensitivity to Bcl-2 inhibitors (TW37) and niclosamide. In BXPC-3 cells, PBK knockdown significantly suppressed NCAPG2 expression and inhibited cell proliferation, migration, and invasion. Co-immunoprecipitation confirmed a direct binding between PBK and NCAPG2.
CONCLUSIONS
PBK is a key regulator of pancreatic cancer and interacts with NCAPG2 to promote tumor progression, suggesting its value as a potential biomarker and therapeutic target for pancreatic cancer.
Humans
;
Pancreatic Neoplasms/genetics*
;
Prognosis
;
Biomarkers, Tumor/genetics*
;
Cell Line, Tumor
;
Cell Proliferation
;
Adenocarcinoma/metabolism*
;
Tumor Microenvironment
;
Cell Movement
;
Mitogen-Activated Protein Kinase Kinases
7.Epigallocatechin gallate attenuates intestinal injury in sepsis by inhibiting apoptosis
Weiwei HUANG ; Tao MA ; Zhihua LI ; Yi WANG ; Xiaoming GAO ; Xiangyou YU
Chinese Journal of Emergency Medicine 2024;33(4):529-535
Objective:To observe the effect of epigallocatechin gallate (EGCG) on intestinal injury in sepsis, and to investigate the effect on endoplasmic reticulum stress (ERS) apoptotic pathway.Methods:Sixty male SD rats were selected and divided into five groups according to the randomized numeric table method: the sham operation group (Sham group), the cecal ligation and puncture sepsis group (CLP group), the sepsis+EGCG low-dose group (postoperative intraperitoneal injection of EGCG 25 mg/kg, EL group), the sepsis+EGCG medium-dose group (postoperative intraperitoneal injection of EGCG 50 mg/kg, EM group), and sepsis+EGCG high-dose group (postoperative intraperitoneal injection of EGCG 75 mg/kg, EH group), each group with 12 rats. The rats in each group were executed 24 h after modeling and specimens were collected. Inflammatory factors in serum were detected by enzyme-linked immunosorbent assay. Pathological changes of ileum were observed under light microscope after hematoxylin eosin staining and evaluated according to the Chiu's score. The intestinal tissues were stained for tight junction protein-1 (CLDN1, Claudin-1), phosphorylated protein kinase R-like endoplasmic reticulum kinase (p-PERK), protein kinase RNA-like endoplasmic reticulum kinase (PERK), cysteinyl aspartate specific protein-12 (Caspase-12), and CCAAT enhancer-binding protein homologous protein (C/EBP-homologous protein antibody, CHOP) protein expression was detected by protein immunoblotting assay. The positive areas of Claudin-1, p-PERK, CHOP, and Caspase-12 in intestinal tissue were detected by immunohistochemistry.Results:Compared with the Sham group, the serum levels of interleukin (IL)-1β, IL-6, tumor necrosis factor-α, and the Chiu's score of rats in the CLP group were increased (all P<0.05). The ileal mucosal tissues showed reduced expression of Claudin-1, ERS apoptosis-associated protein p-PERK, CHOP, and Caspase-12 expression were increased (all P<0.05). Compared with the CLP group, the intestinal injury in rats was alleviated after the administration of low, medium and high dose EGCG intervention (all P<0.05). The serum inflammatory factor level, Chiu's score and the protein expression level and positive area of ERS apoptosis-related proteins, p-PERK, CHOP, and Caspase-12 in the small intestinal tissues of EL group were further reduced compared with that of the CLP group were further decreased, and EM group was further decreased than EL group, and EH group was further decreased than EM group (all P<0.05). The protein expression level and positive area of Claudin-1 in small intestinal tissues of EL group were further increased compared with that of CLP group (both P<0.05), and EM group was further increased compared with that of EL group and EH group was further increased compared with EM group (all P<0.05). Conclusions:EGCG may have a protective effect on intestinal injury in septic rats by inhibiting the activation of ERS-induced apoptotic pathway, and the efficacy of high-dose EGCG has a better effect.
8.Determination of tryptophan metabolite levels in serum and urine from adolescents with depression by liquid chromatogra-phy-tandem mass spectrometry
Mengmeng MA ; Xiaoming TENG ; Liu LU ; Zhihan YE ; Ming ZONG
Chinese Journal of Clinical Laboratory Science 2024;42(8):561-566
Objective To observe and compare the concentrations of tryptophan-kynurenine pathway metabolites in serum and urine of adolescents with depression individuals using liquid chromatography-tandem mass spectrometry(LC-MS/MS).Methods The major metabolites in this pathway,such as tryptophan(TRP),kynurenine(KYN),kynurenic acid(KYNA),and 3-hydroxykynurenine(3-HK)were quantitatively analyzed using isotope-labeled internal standards.The separation was achieved using a Shimadzu C18 col-umn with gradient elution of 0.2%aqueous acid and acetonitrile.The detection was performed within 7 minutes using positive ion mode and multiple reaction monitoring(MRM).The parameters,such as linear range and precision were evaluated to assess reliability of the method.Subsequently,this method was applied to detect and compare the results in the samples of serum and urine from 143 adoles-cents with depression and 110 healthy controls.Results Taking TRP as the example,the linear ranges for serum and urine were 0.54 to 107.84 μmol/L and 0.74 to 147.06 μmol/L,respectively.The intra-batch coefficient of variation(CV)was ≤6.3%,the inter-batch CV was ≤3.22%,and the total laboratory CV was ≤6.5%.The results showed the KYNA,KYN and TRP levels were lower in the de-pression group compared to the control group,while 3-HK levels were higher in the depression group with statistical significance(P<0.01).Apart from TRP,the levels of other metabolites were significantly higher in urine than those in serum,with statistical signifi-cance(P<0.01).Conclusion Compared to the results of serum,the concentrations of TRP metabolites,including KYN,KYNA and 3-HK were higher than those in urine.The concentrations of TRP-KP metabolites in urine,i.e.,KYN,KYNA and 3-HK were higher than those in serum,and the detection of TRP-KP metabolites in urine may offer a greater advantage because the urine collection process is non-invasive.
9.Guidelines for the operation of imaging equipment in orbital diseases(2024)
Yi SHAO ; Jianmin MA ; Xiaoming HUANG ; Xiaoming HUANG ; Xiaoming HUANG ; Xiaoming HUANG ; Xiaoming HUANG ; Xiaoming HUANG
International Eye Science 2024;24(2):171-181
Orbital disorders include conditions originating from the orbital bones, surrounding tissues, and post-orbital septum. They also include systemic ailments affecting the orbit. Different clinical symptoms make up the complex range of orbital disorders. Because these disorders mostly impact the orbital area instead of the intraocular compartment, there is little diagnostic usefulness for typical ophthalmic visual tests. As such, the primary instruments for diagnosing and evaluating orbital illnesses have become ophthalmic imaging modalities, including ocular ultrasonography(B-scan), computed tomography(CT), and magnetic resonance imaging(MRI). One way to improve the precision and promptness of diagnosing orbital diseases is to standardize the functioning of widely used imaging equipment and define the radiological features of orbital abnormalities. Such programs are crucial for the care of patients with orbital disorders since they considerably reduce the number of misdiagnoses and missed diagnoses in these individuals. The underlying concepts, operational techniques, and normal and pathological imaging findings associated with common diagnostic tools for orbital illnesses are all thoroughly reviewed in this guideline. The objective is to improve primary healthcare settings' diagnostic competence in the field of orbital pathology and to standardize procedures for diagnosing orbital disorders.
10.The application of family empowerment model on the primary caregivers of first-episode stroke dysphagia patients
Hong YU ; Jing DU ; Qian XU ; Mingming XU ; Xiangge FAN ; Fan ZHANG ; Xueyun WENG ; Xiaoming MA ; Yanhua HOU ; Linqing LI
Chinese Journal of Practical Nursing 2024;40(4):263-271
Objective:To explore the effect of family empowerment model on the improvement of swallowing care ability and care preparedness of primary caregivers of first-episode stroke dysphagia patients, further to explore its impact on patients′s wallowing function and life quality.Methods:This study was a randomized controlled study. From January 2021 to December 2022, 80 main caregivers of patients with dysphagia caused by manual stroke admitted to the Department of Acupuncture and Moxibustion, Shenzhen Hospital of Traditional Chinese Medicine were selected as the research objects, and 40 cases in the control group and 40 cases in the observation group were selected by random number table method. The control group were treated with conventional nursing care of first-episode stroke dysphagia patients in the acupuncture and moxibustion Department. On the basis of the conventional care in the control group, the observation group were treated with family empowerment model intervention for 14 days and was followed up for 28 days. Primary caregivers′ swallowing care ability, Caregiver Preparedness Scale (CPS), patients′ swallowing function rate, Swallowing Related Quality of Life (SWALQOL) were used to evaluate the effects before intervention and at the end of intervention.Results:There were 18 males and 19 females primary caregivers in the control group, aged (55.61 ± 7.43) years old. There were 18 males and 21 females primary caregivers in the observation group, aged (58.23 ± 8.22) years old. The swallowing care ability score showed a statistically significant difference between the observation group (143.47 ± 3.96) and the control group (107.74 ± 1.43) ( t=-26.76, P<0.05). After intervention, the caregiver preparedness scale was (26.11 ± 3.81) in the observation group, and (18.35 ± 4.54) in the control group, and the difference was statistically significant ( t=-4.11, P<0.05).The patients′ swallowing function rate and SWALQOL score were respectively 97.44% (38/39) and (91.41 ± 8.08) points in the observation group, and 72.97% (27/37) and (80.33 ± 4.21) points in the control group, and the difference was both statistically significant ( χ2=10.76, t=-2.54, both P<0.05). Conclusions:The implementation of family empowerment model could enhance the swallowing care ability and care preparedness of primary caregivers of the first-episode stroke dysphagia patients, which could further improve patients′ swallowing function and life quality.

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